Hello, I collected As K EXAFS data and created a cluster which could represent the "probable geometry". I have an ATOMS file with coordinates of the atoms in a triclinic unit cell. ATOMS did its thing but FEFF refused to process the data and generated an error: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP Then I filled the empty space around the cluster with hydrogen atoms on a grid, hoping that FEFF would like it more, but the same error came. Short of creating a complete structure (of some sort) with the cluster embedded in it, what can I do to make this work? Thank you, Juro Majzlan ---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de
Juro, this sounds like a problem with the FEFF input. You get this message if you specify absorbers in the POTENTIALS section but not list them in the ATOMS section. Example (for gold oxide): If you do POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 79 Au -1 -1 0.01 1 8 O -1 -1 3 2 79 Au -1 -1 2 ATOMS 0.00000 0.00000 0.00000 0 Au1 0.00000 0.58748 -1.39811 1.19247 1 O2 1.92920 1.64570 1.05726 0.47284 1 O1 2.01239 -1.56105 -1.22348 -0.48666 1 O1 2.04220 -0.47075 1.40652 -1.44616 1 O1 2.07154 it will complain that there is no atom for unique potential 2. If you add 1.17495 -2.79622 0.00000 2 Au1 3.03304 it will do the job. If you post the atoms and feff input files I can have a closer look. Norbert -- Dr. rer. nat. Norbert Weiher (norbert.weiher@manchester.ac.uk) School of Chemical Engineering and Analytical Science Sackville Street, Manchester, M60 1QD - Phone: +44 161 306 4468
Juraj, Please post the feff.inp file. You might also send the atoms.inp file. -Matt On Thu, 21 Jul 2005, Juraj Majzlan wrote:
Hello,
I collected As K EXAFS data and created a cluster which could represent the "probable geometry". I have an ATOMS file with coordinates of the atoms in a triclinic unit cell. ATOMS did its thing but FEFF refused to process the data and generated an error: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP
Then I filled the empty space around the cluster with hydrogen atoms on a grid, hoping that FEFF would like it more, but the same error came.
Short of creating a complete structure (of some sort) with the cluster embedded in it, what can I do to make this work?
Hello,
thank you for the fast response. According to Norbert's
suggestion, I looked in the feff file. The problem seems to
be with the potential 1, assigned to As. Removing this line
and rewriting all potentials in the list makes feff like
the input. However, I don't understand why ATOMS has
generated these ipot values. The atoms.inp is below.
Juro
----------------------------------part of feff.inp
POTENTIALS
* ipot Z element
0 33 As
1 33 As
2 8 O
3 26 Fe
ATOMS * this list contains 24
atoms
* x y z ipot tag
distance
0.00000 0.00000 0.00000 0 As
0.00000
-1.40201 0.76410 -0.53997 2 O3_1
1.68554
0.00000 -1.59002 -0.56202 2 O4_1
1.68643
0.00000 -0.00003 1.68705 2 O1_1
1.68705
1.37801 0.79495 -0.56207 2 O2_1
1.68724
-2.86303 -0.03582 -1.71095 3 Fe2_1
3.33550
-1.39501 -2.50095 -1.71100 3 Fe3_1
3.33591
-1.46101 -0.86989 -2.91804 2 O13_1
3.37731
-2.86203 -1.70487 -0.55592 2 O12_1
3.37740
0.00000 -0.69408 3.59511 3 Fe1_1
3.66150
0.00000 -2.60210 2.90109 2 O7_1
3.89708
2.03002 -0.69418 3.59504 2 O9_1
4.18655
-2.03002 -0.69397 3.59518 2 O8_1
4.18663
-2.86503 1.63323 -2.86599 2 O11_1
4.36918
0.07200 -3.29702 -2.86609 2 O15_1
4.36921
-4.26604 0.79825 -0.50387 2 O10_1
4.36923
-1.32901 -4.13200 -0.50397 2 O14_1
4.36963
0.00000 1.21295 4.28913 2 O6_1
4.45734
0.00000 -1.38895 -4.49813 2 O5_1
4.70769
-2.79603 -3.41087 -2.86399 2 O17_1
5.25873
-4.33104 -0.83474 -2.86393 2 O16_1
5.25897
0.00000 -1.38912 5.50217 2 O5_2
5.67482
5.73406 0.79772 -0.50422 2 O10_2
5.81120
0.00000 1.21312 -5.71117 2 O6_2
5.83859
END
----------------------------------atoms.inp
title model6
space P 1
rmax=6.0 a=10.0001 b=10.0002 c=10.0003 alpha=90.001
beta=90.002 gamma=90.003
core=As
atom
! At.type x y z tag
As 0.00000 0.00000 0.00000 As
Fe 0.00000 -0.06940 0.35950 Fe1
Fe -0.28630 -0.00360 -0.17110 Fe2
Fe -0.13950 -0.25010 -0.17110 Fe3
O 0.00000 0.00000 0.16870 O1
O 0.13780 0.07950 -0.05620 O2
O -0.14020 0.07640 -0.05400 O3
O 0.00000 -0.15900 -0.05620 O4
O 0.00000 -0.13890 0.55020 O5
O 0.00000 0.12130 0.42890 O6
O 0.00000 -0.26020 0.29010 O7
O -0.20300 -0.06940 0.35950 O8
O 0.20300 -0.06940 0.35950 O9
O -0.42660 0.07980 -0.05040 O10
O -0.28650 0.16330 -0.28660 O11
O -0.28620 -0.17050 -0.05560 O12
O -0.14610 -0.08700 -0.29180 O13
O -0.13290 -0.41320 -0.05040 O14
O 0.00720 -0.32970 -0.28660 O15
O -0.43310 -0.08350 -0.28640 O16
O -0.27960 -0.34110 -0.28640 O17
On Thu, 21 Jul 2005 08:53:27 -0500 (CDT)
Matt Newville
Juraj,
Please post the feff.inp file. You might also send the atoms.inp file.
-Matt
On Thu, 21 Jul 2005, Juraj Majzlan wrote:
Hello,
I collected As K EXAFS data and created a cluster which could represent the "probable geometry". I have an ATOMS file with coordinates of the atoms in a triclinic unit cell. ATOMS did its thing but FEFF refused to process the data and generated an error: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP
Then I filled the empty space around the cluster with hydrogen atoms on a grid, hoping that FEFF would like it more, but the same error came.
Short of creating a complete structure (of some sort) with the cluster embedded in it, what can I do to make this work?
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de
On Thursday 21 July 2005 09:51, Juraj Majzlan wrote:
thank you for the fast response. According to Norbert's suggestion, I looked in the feff file. The problem seems to be with the potential 1, assigned to As. Removing this line and rewriting all potentials in the list makes feff like the input. However, I don't understand why ATOMS has generated these ipot values. The atoms.inp is below.
Juro, You are seeing a known bug in Atoms that has been discussed before on the mailing list. Here is one example: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2004-March/000756.html Rooting through the archives, you will find several other times that this has come up. The work around is to make rmax bigger in Atoms. The real soution is for me to stop being so darn lazy and fix the problem. ;-) B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
participants (4)
-
Bruce Ravel -
Juraj Majzlan -
Matt Newville -
Norbert Weiher